Ecosyste.ms: Papers

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.1038/s41598-020-80165-9

Multi-level remodelling of chromatin underlying activation of human T cells
Cited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: almost 4 years ago

10.1371/journal.ppat.1009374

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event
Cited by: 31
Author(s): Madlen Stange, Alfredo Mari, Tim Roloff, Helena M. B. Seth-Smith, Michael Schweitzer, Myrta Brunner, Karoline Leuzinger, Kirstine Kobberøe Søgaard, Alexander Gensch, Sarah Tschudin‐Sutter, Simon Fuchs, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Rita Schneider-Sliwa, Manuel Battegay, Hans H. Hirsch, Adrian Egli
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: about 4 years ago

10.1186/s13104-019-4473-z

RepViz: a replicate-driven R tool for visualizing genomic regions
Cited by: 0
Author(s): Thomas Faux, Kalle T. Rytkönen, Asta Laiho, Laura L. Elo
Software Mentions: 8
Published: over 5 years ago

10.1186/s12859-019-2610-2

BPG: Seamless, automated and interactive visualization of scientific data
Cited by: 55
Author(s): Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Davina Mak, Felix Lam, Marco A. Albuquerque, Yaoguo Wu, Esther Jung, Maud H.W. Starmans, Michelle Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang, Emilie Lalonde, Syed Haider, Nicole A. Simone, Dorota H. Sendorek, Kenneth C. Chu, Nathalie C. Moon, Natalie S. Fox, Michal R. Grzadkowski, Nicholas J. Harding, Clement Fung, Amanda R. Murdoch, Kathleen E. Houlahan, Jianxin Wang, David R. Garcia, Richard de Borja, Ren Sun, Xihui Lin, Gregory M. Chen, Aileen Lu, Yu-Jia Shiah, Amin Zia, Ryan Kearns, Paul C. Boutros
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41416-018-0236-1

Phenotype-independent DNA methylation changes in prostate cancer
Cited by: 11
Author(s): Davide Pellacani, Alastair Droop, Fiona M. Frame, Matthew Simms, Vincent M. Mann, Anne T. Collins, Connie J. Eaves, Norman J. Maitland
Software Mentions: 6
Published: about 6 years ago

10.1186/s12859-020-03818-6

Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Cited by: 2
Author(s): Meng Li
Software Mentions: 6
Published: about 4 years ago

10.1038/s41438-021-00648-2

Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach
Cited by: 22
Author(s): Qiuping Tan, Sen Li, Yuzheng Zhang, Min Chen, Binbin Wen, Shan Jiang, Xiude Chen, Xiling Fu, Dongmei Li, Wu H, Yong Wang, Wei Xiao, Ling Li
Software Mentions: 5
Published: about 3 years ago

10.3389/fnins.2021.622640

Integrated Multi-Omic Analyses of the Genomic Modifications by Gut Microbiome-Derived Metabolites of Epicatechin, 5-(4′-Hydroxyphenyl)-γ-Valerolactone, in TNFalpha-Stimulated Primary Human Brain Microvascular Endothelial Cells
Cited by: 13
Author(s): Karla Fabiola Corral-Jara, Saivageethi Nuthikattu, John C. Rutledge, Amparo C. Villablanca, Christine Morand, Hagen Schroeter, Dragan Milenković
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-07322-2

Environmental RNAi pathways in the two-spotted spider mite
Cited by: 10
Author(s): Mosharrof Mondal, Jacob Peter, Obrie Scarbrough, Alex S. Flynt
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12711-020-00553-7

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems
Cited by: 38
Author(s): Samuele Bovo, Anisa Ribani, María Muñoz, E. Alves, J. P. Araújo, Rıccardo Bozzi, Marjeta Čandek-Potokar, Rui Charneca, Federica Di Palma, Graham Etherington, Ana Fernández, Fabián García, Juan García‐Casco, Danijel Karolyi, M. Gallo, Vladimir Margeta, J.M. Martins, Marie J. Mercat, Giulia Moscatelli, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaitė, Juliette Riquet, Radomir Savić, Giuseppina Schiavo, G. Usai, Valerio Joe Utzeri, Christoph Zimmer, Cristina Óvilo, Luca Fontanesi
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-58985-6

Facilitating gene editing in potato: a Single-Nucleotide Polymorphism (SNP) map of the Solanum tuberosum L. cv. Desiree genome
Cited by: 33
Author(s): François Sevestre, Maud Facon, Fabrice Wattebled, Nicolas Szydlowski
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.32724

RNA-dependent RNA targeting by CRISPR-Cas9
Cited by: 145
Author(s): Steven Strutt, Rachel M Torrez, Emine Kaya, Oscar Negrete, Jennifer A. Doudna
Software Mentions: 3
Published: almost 7 years ago

10.1093/bib/bbv097

In the loop: promoter–enhancer interactions and bioinformatics
Cited by: 80
Author(s): Antonio M. Mora, Geir Kjetil Sandve, Odd S. Gabrielsen, Ragnhild Eskeland
Software Mentions: 2
Published: almost 9 years ago

10.1007/s10577-016-9546-4

Capturing genomic relationships that matter
Cited by: 3
Author(s): Cameron S. Osborne, Borbála Mifsud
Software Mentions: 2
Published: almost 8 years ago

10.1093/bioinformatics/btu379

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
Cited by: 172
Author(s): Douglas H. Phanstiel, Alan P. Boyle, Carlos L. Araya, M Snyder
Software Mentions: 1
Published: over 10 years ago

10.1186/s13100-018-0130-7

sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data
Cited by: 19
Author(s): Romain Pogorelcnik, Chantal Vaury, Pierre Pouchin, Silke Jensen, Emilie Brasset
Software Mentions: 1
Published: over 6 years ago